What is the vaginal microbiome?

By Gabrielle Gleeson-Solomon, CEO of Tota
Scientific Review by Dr Nick Parkinson, PhD

Updated: 10th September 2026

Ask Tota: What is the vaginal microbiome?

The vaginal microbiome isn't new. Our understanding of it is.

Most of us grew up learning about periods, contraception, pregnancy and STIs. Almost none of us were told that the vagina comes with its own built-in defence system, helping to keep harmful bacteria in check.

Back in 1892, a German gynaecologist called Albert Döderlein looked at samples from healthy women  and found the same type of bacteria time and time again: what's now known as Lactobacillus. He worked out these bacteria were making the vagina slightly acidic, and that acidity was helping to keep harmful bacteria out.

He was right. We still teach that today.

And then the science barely moved. Women's health has always been under-researched, and the vagina was no exception. For over a century, the vagina was filed away as simple: one group of bacteria doing one job. It took DNA sequencing, in the last 15 years, to show that Döderlein's bacteria were only one part of something much bigger: a whole ecosystem of microorganisms living in the vagina.

That ecosystem turns out to matter for far more than the odd bout of thrush. It's connected to bacterial vaginosis, recurrent UTIs, fertility, and how your body changes at different life stages, including menopause.

What the vaginal microbiome actually is

The vaginal microbiome is the community of bacteria, fungi and other microorganisms living in the vagina. Billions of them.

"Bacteria" tends to make people think of illness, but most of these aren't harmful at all. Plenty are working for you, protecting the space and making it harder for less welcome microbes to move in. It's the same idea as the good bacteria in your gut that everyone's talking about. A healthy vagina is a busy, balanced ecosystem.

Lactobacillus still does much of the heavy lifting, exactly as Döderlein discovered back in 1892, and there isn't one single species that means healthy. Several different Lactobacillus species can each dominate a healthy vagina, most commonly L. crispatus, L. gasseri, L. jensenii and L. iners.

In short, the vaginal microbiome is:

• A community of bacteria and other microorganisms living in the vagina

• Usually, but not always, rich in Lactobacillus species before menopause

• Influenced by hormones, age, lifestyle, diet, medication and other factors

• Connected to vaginal, urinary and reproductive health

• Dynamic, meaning it can change throughout your life
  

No two vaginal microbiomes are the same

Just as no two people are identical, no two microbiomes are either. Lactobacillus leads the way in most healthy vaginas, but the exact line-up shifts from woman to woman. There's no single perfect vaginal microbiome, or exact definition of a healthy one.

Scientists look at several factors when assessing a vaginal microbiome, including:

• Which microorganisms are present

• Their abundance relative to one another

• Whether potentially protective bacteria are present

• Whether there is an increase in bacteria associated with conditions such as bacterial vaginosis

A microbiome result should be interpreted as part of a wider health picture, not as a diagnosis on its own.

Vaginal microbiomes change over time, too. Menstrual cycles, hormones, sex, antibiotics, pregnancy, menopause and plain old illness can all shift the balance of microbes, changing which ones become more or less dominant over time.

Other factors that may affect its composition include diet, lifestyle (such as smoking or excessive drinking), hormonal contraception, vaginal products and douching, and infections or other health conditions.

That's completely normal. The microbiome is surprisingly tough, and most of the time it rights itself without any intervention at all - it really is a built-in defence system!

When the balance shifts: BV and related symptoms

However, sometimes the vaginal microbiome can't get itself back to where it was. If the Lactobacillus bacteria drop off and other microbes manage to take over, it can create a suboptimal environment.  

When the protective bacteria don't bounce back, there's more room for less welcome bacteria and yeast to grow. That can mean bacterial vaginosis (BV), thrush, and for some women, UTIs that keep returning.

BV is associated with a change in the balance of vaginal bacteria, often involving fewer lactobacilli and an increase in several other types of bacteria, such as gardnerella. It may cause a thin, greyish-white discharge and a strong or fishy smell, although around half of women with BV have no symptoms. BV isn't simply the presence of one bacterium, it usually involves a broader shift in the vaginal environment.

And symptoms don't always tell the full story. Two women with the same symptoms can have completely different microbiomes behind them, and plenty of women whose Lactobacillus has dropped off feel perfectly fine. So a suboptimal vaginal microbiome can be causing trouble in the background without any obvious signs. That's part of why it's worth knowing what's actually in there, rather than waiting for symptoms to appear.

Microbiome testing should not be used to self-diagnose BV. If you have unusual discharge, odour, irritation, pelvic pain or other new symptoms, speak to your healthcare professional.

Vaginal and urinary health

The vagina, urethra and bladder are close neighbours, and their microbial communities can overlap. Bacteria associated with UTIs may first colonise the area around the vagina before entering the urinary tract.

Research has linked lower levels of some vaginal Lactobacillus species with an increased risk of UTIs, particularly after menopause. This doesn't mean an altered vaginal microbiome is always the cause of a UTI, recurrent urinary symptoms can have several possible explanations. But if infections or symptoms keep returning, understanding both the vaginal and urinary microbiomes may provide an additional piece of information, especially when routine testing hasn't explained the pattern.

Historically, urine was considered sterile. We now know the bladder can contain its own community of microorganisms, the urinary microbiome. It isn't identical to the vaginal microbiome, but research suggests the two can share some organisms and influence one another, which is one reason to look at both together.

A vaginal microbiome test cannot diagnose an acute UTI and is not a replacement for clinical assessment. If you currently have UTI symptoms, seek advice from a healthcare professional.

Can a vaginal microbiome test diagnose a UTI?

No. A vaginal microbiome test cannot diagnose an acute UTI and is not a replacement for clinical assessment. If you currently have UTI symptoms, seek advice from a healthcare professional. 

Vaginal microbiome and fertility

This is the part we find really interesting and where the research is moving fastest.

The vagina sits directly below the cervix and the womb, so the balance of microbes in the vagina may influence the rest of the reproductive system. Researchers are increasingly exploring the relationship between vaginal bacteria and fertility, including how the vaginal microbiome might influence embryo implantation and pregnancy.

Researchers are also investigating the relationship between vaginal dysbiosis (BV) and implantation, with several IVF studies suggesting that women with disrupted vaginal microbiomes have lower implantation rates. BV is getting particular attention because a growing body of research shows that plenty of women with BV have no symptoms at all, so a disrupted microbiome can be sitting there unnoticed while fertility journeys and treatment go ahead.

It's worth being clear that this is early science and the research is still ongoing. For now these are associations rather than proven causes. Fertility depends on many interconnected factors, including ovulation, egg and sperm health, the fallopian tubes, the uterus, embryo development, age and general health.

A microbiome test cannot predict or promise a pregnancy. What it can do is show you what's actually there, so anything unusual can be identified early and discussed with your doctor or clinic, rather than after months of trying, or the cost of a treatment cycle.

What happens to the vaginal microbiome during menopause?

During perimenopause and menopause, falling oestrogen levels can change the vaginal tissues, acidity and microbiome. Oestrogen helps support glycogen within vaginal cells, which helps create conditions in which many Lactobacillus species can thrive. As oestrogen levels fall, the vaginal microbiome may contain fewer lactobacilli and become more diverse, and vaginal pH may also rise.

These biological changes can be connected with symptoms such as vaginal dryness or irritation, burning or soreness, pain during sex, urinary urgency or frequency, pain when urinating, and recurrent UTIs. These symptoms may form part of genitourinary syndrome of menopause, often shortened to GSM.

A microbiome test cannot diagnose GSM. However, it may provide additional information about how the vaginal and urinary environment has changed, which you can then discuss with your doctor or a healthcare professional with expertise in menopause. You do not have to accept vaginal or urinary symptoms as an inevitable part of getting older, treatments and support are available.

Why isn't the vaginal microbiome common knowledge yet?

The honest answer is that this science is very new. The tools to see the vaginal microbiome properly have only existed for about fifteen years, mostly within academic research settings. Most of what we know about the vaginal microbiome has been discovered since then. It's a rapidly evolving and exciting field, with new discoveries continuing to shape our understanding of the vaginal microbiome.

Even medical training, guidelines and everyday testing are working hard to catch up. Plenty of doctors were never taught any of this in med school because it wasn't in the textbooks when they trained. 

Add to that a century of the vagina being treated as simple and women's health being under-researched, and it's not hard to see how something this important went unmentioned.

What testing can and can't tell you

Vaginal microbiome testing can show which microorganisms were detected in a sample, and their abundance relative to one another. Tota also offers full quantification. Depending on the testing method, it may help show whether the microbiome is dominated by Lactobacillus, which species are present, whether other bacteria are present in higher or lower proportions, how mixed the overall pattern is, and how the vaginal and urinary microbiomes compare, if both are tested.

Traditional tests often look for particular organisms that are already suspected. Tota uses non-targeted DNA sequencing to look broadly across the microbial DNA detected in your sample, rather than checking only a predefined shortlist. This provides a broader picture of what's there, translated into plain English so you can discuss it with your healthcare professional.

It can't diagnose every cause of vaginal or urinary symptoms, confirm or rule out a UTI, replace STI testing, cervical screening or a clinical examination, tell you whether you'll become pregnant, predict IVF success or embryo implantation, prove a particular microorganism caused a symptom, or tell you which treatment is right for you without clinical context. Microbiome testing provides information. It should support appropriate healthcare, not replace it.

You may want to explore vaginal and urinary microbiome testing if you experience recurrent urinary symptoms, BV or vaginal symptoms keep returning, you have an ongoing pattern that hasn't been explained, you're preparing for fertility treatment and want additional information, you've noticed vaginal or urinary changes during menopause, or you simply want to understand your body better.

Tota is rarely someone's first step. It's often the point people reach after repeated appointments, tests or treatments have left them without a clear explanation. When you've tried everything, understanding more may be the next step.

Why this matters

The science now exists to show women what's actually going on in their own bodies. Not just when something goes wrong, but what's normal for them, how it changes over time, and what may be contributing to the symptoms that keep coming back.

That shouldn't be specialist knowledge. It should be something every woman gets told.

We're on a mission at Tota to give women the information they deserve about their bodies.

When might someone consider testing their vaginal microbiome?

You may want to explore vaginal and urinary microbiome testing if:

• You experience recurrent urinary issues
• BV or vaginal issues keep returning
• You have an ongoing pattern which hasn’t been explained
• You are preparing for fertility treatment and want additional information
• You have noticed vaginal or urinary changes during menopause
• You simply want to understand your body better
  

Tota is rarely someone’s first step. It is often the point they reach after repeated appointments, tests or treatments have left them without a clear explanation.

When you have tried everything, understanding more may be the next step.

Explore About Our Tests →

Frequently asked questions

Is the vaginal microbiome the same as vaginal flora?

Yes. Vaginal flora is an older term for the microorganisms living in the vagina. Vaginal microbiota refers to the microorganisms themselves, while vaginal microbiome can also include their genes and surrounding biological environment. In everyday use, the terms are often used interchangeably.

Is Lactobacillus always good?

Not necessarily. Many Lactobacillus species help maintain an acidic vaginal environment and are associated with vaginal health. However, different species behave differently, and a healthy vaginal microbiome is not identical in every woman. It’s also possible to experience lactobacillus overgrowth which is too much of it. A microbiome test result needs to be interpreted in context.

Does having lots of different vaginal bacteria mean my microbiome is healthier?

Not necessarily. Unlike the gut, where greater bacterial diversity is often viewed positively, a highly diverse vaginal microbiome can be associated with disruption. However, diversity alone cannot diagnose a health problem.

Can the vaginal microbiome cause a UTI?

The vaginal microbiome may affect susceptibility to UTIs, but it is not the only factor involved. A microbiome test cannot confirm an acute infection or prove why a UTI occurred.

The full picture, finally in your hands

Your vaginal microbiome is not a verdict on your health. It is one part of a much bigger picture.

But when symptoms keep returning, your body is changing or standard tests have not provided an explanation, seeing more may help you ask better questions and have more informed conversations.

Because women deserve better answers.

Explore Vaginal Microbiome Testing →

This article is for general information and is not medical advice. Tota microbiome testing is designed to complement, not replace, clinical testing, diagnosis or treatment.

Sources

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2. Hugenholtz F, van der Veer C, Terpstra ML, Borgdorff H, van Houdt R, Bruisten SM, et al. Urine and vaginal microbiota compositions of postmenopausal and premenopausal women differ regardless of recurrent urinary tract infection and renal transplant status. Sci Rep. 2022;12. Scientific Reports
3. European Society of Human Reproduction and Embryology (ESHRE). Good practice recommendations on recurrent implantation failure. Hum Reprod Open. 2023;2023(3):hoad023. Human Reproduction Open
4. Graspeuntner S, et al. Vaginal microbial community state types fail to predict IVF treatment outcome. Hum Reprod Open. 2026;2026(2):hoag018. Human Reproduction Open
5. Nieto MR, et al. Menopausal shift on women’s health and microbial niches. npj Women's Health. 2025. Nature
6. NHS. Urinary tract infections (UTIs). NHS
7. NHS. Bacterial vaginosis. NHS
8. Ventolini G. Progresses in vaginal microflora physiology and implications for bacterial vaginosis and candidiasis. Womens Health (Lond). 2016;12(3):283-291. Women's Health
9. Dubé-Zinatelli E, Cappelletti L, Ismail N. Vaginal microbiome: environmental, biological, and racial influences on gynecological health across the lifespan. Am J Reprod Immunol. 2024;92(6):e70026. American Journal of Reproductive Immunology
10. Skafte-Holm A, Humaidan P, Bernabeu A, Lledo B, Jensen JS, Haahr T. The association between vaginal dysbiosis and reproductive outcomes in sub-fertile women undergoing IVF-treatment: a systematic PRISMA review and meta-analysis. Pathogens. 2021;10(3):295. Pathogens
    

This article is for general information and does not replace medical advice. If you're experiencing new, severe, persistent or worsening symptoms, please speak to a GP or another qualified healthcare professional.